Diagnostic Biomarker For Breast Cancer Research Articles

Study of NALT1 and CTBP1-AS1 lncRNAs expression levels in triple-negative breast cancer patients in the Iranian population

BackgroundTriple-negative breast cancer (TNBC), an aggressive subtype with a poor prognosis, is notably difficult to treat. Emerging research highlights the significant roles of long non-coding RNAs (lncRNAs) in cancer biology. LncRNAs, such as NALT1 and CTBP1-AS1 are implicated in oncogenic processes; this study hypothesizes that NALT1 and CTBP1-AS1 are overexpressed in TNBC tissues compared to adjacent non-tumor tissues and may serve as biomarkers. Methods: One hundred pairs of tumor and adjacent non-tumor tissues were obtained from female patients with triple-negative breast cancer. After extracting RNA, cDNA synthesis was carried out for all samples. Quantitative real-time PCR (qRT-PCR) was employed to assess differential gene expression. Results: The expression of NALT1 (p-value <0.0001) and CTBP1-AS1 (p-value <0.0002) lncRNAs increased in TNBC tumor tissues in comparison to adjacent non-tumor tissues. A statistically positive correlation (ρ = 0.5844, p < 0.0001) was observed between the expression levels of NALT1 and CTBP1-AS1 in breast cancer patients. The ROC analysis indicated that NALT1 (AUC = 0.718, specificity = 61 %, sensitivity = 70 %) shows moderate potential and CTBP1-AS1 (AUC = 0.648, specificity = 65 %, sensitivity = 55 %) exhibits poor potential as a diagnostic biomarker for breast cancer. Conclusion: This study shows that NALT1 and CTBP1-AS1 lncRNAs are upregulated in TNBC tissues. Additionally, a positive correlation exists between their expression levels in breast cancer. Further research is needed to understand their mechanisms as molecular biomarkers.

The Analysis of Plasma Proteomics for Luminal A Breast Cancer.

Breast cancer is the prevailing malignancy among women, exhibiting a discernible escalation in incidence within our nation; hormone receptor-positive (HR+) human epidermal growth factor receptor 2-negative (HER2-) breast cancer is the most common subtype. In this study, we aimed to search for a non-invasive, specific, blood-based biomarker for the early detection of luminal A breast cancer through proteomic studies. To explore new potential plasma biomarkers, we applied data-independent acquisition (DIA), a technique combining liquid chromatography and tandem mass spectrometry, to quantify breast cancer-associated plasma protein abundance from a small number of plasma samples in 10 patients with luminal A breast cancer, 10 patients with benign breast tumors, and 10 healthy controls. The proteomes of 30 participants in all cohorts were analyzed using the DIA method, and a total of 517 proteins and 3584 peptides were quantified. We found that there were significant differences in plasma protein expression profiles between breast cancer patients and non-breast cancer patients, and breast cancer was mainly related to lipid metabolism pathways. Finally, the optimal protein combinations for the diagnosis of breast cancer were PON3, IGLV3-10, and IGHV3-73 through multi-model analysis, which had a high prediction accuracy for breast cancer (AUC = 0.92), and the model could also distinguish breast cancer from HC (AUC = 0.92) and breast cancer from benign breast tumor (AUC = 0.91). The study revealed proteomic signatures of patients with luminal A breast cancer, identified multiple differential proteins, and identified three plasma proteins as potential diagnostic biomarkers for breast cancer. It provides a reference for the screening of biomarkers for breast cancer.

Detection of Catalase and 4-Hydroxynonenal as Detective Biomarkers in Iraqi Breast Cancer

Breast cancer is the most common malignant tumor among women and a leading cause of cancer-related death. Early diagnosis is critical for improving treatment outcomes. The objective of this study is to determine and examine catalase (CAT) and 4-hydroxynonenal (4-HNE) markers as non-invasive biomarkers for early detection in Iraqi breast cancer. A case-control study of 150 participants was further divided into 75 women with a diagnosis of breast cancer and 75 healthy controls. In the present study, blood samples were collected for the determination of serum CAT and 4-HNE levels using an enzyme-linked immunosorbent assay technique. The biochemical markers urea and creatinine were determined by automated Cobas c311. Hemoglobin concentration (HB)-and total white blood cell (WBC) count was done by an automated hematology analyzer. Statistical analyses were performed using the SPSS version 24, where receiver operating characteristics (ROC) analysis was used to assess diagnostic performance. CAT activity was significantly reduced in the patient group (6.07±1.19 pg/ml) compared to controls (12.11±2.74 pg/ml), while 4-HNE was significantly elevated in the patient group (11.43±2.41 pg/ml) compared to control (3.83±1.02 pg/ml). Among hematology analyzer, there was a significant difference in HB and WBC between patients and controls. Roc analyses demonstrated a sensitivity of 100% for CAT and 98% for 4-HNE. Reduced serum levels of CAT and elevated 4-HNE levels in Iraqi breast cancer may serve as new diagnostic biomarkers for breast cancer, highlighting their role in disease progression.

Serum exosomal miR-200c is a potential diagnostic biomarker for breast cancer

Background Breast cancer (BC) is one of the most common malignancies in women. Exosomes are widely found in body fluids and carry microRNAs (miRNAs) that reflect the biological properties of the parental cells. Our study aimed to investigate the differential expression of miR-200c in BC serum exosomes and its diagnostic value. Methodology miRNA profiles in culture supernatant exosomes of normal mammary epithelial cells MCF-10A and BC cells (MCF-7, MDA-MB-231, MCF-7 Taxol) were examined by miRNA deep sequencing to screen for significantly differentially expressed miRNAs; Transmission electron microscopy (TEM), Nanoparticle tracking analysis (NTA), and Western blot were used to identify exosomes; qPCR was used to detect the expression level of miR-200c in cellular exosomes and serum exosomes; The efficacy of individual and combined tests of each indicator to diagnose BC was evaluated using receiver operating characteristic (ROC) curves. Results We identified typical exosome features by TEM, NTA and Western blot, indicating successful exosome extraction. Then our miRNA sequencing results and qRT-PCR experiments showed that miR-200c was significantly down-regulated in BC cell exosomes. In addition, we divided the clinical serum samples into two cohorts according to region, and in independent cohort I, the serum exosomal miR-200c levels of BC patients were significantly lower than those of healthy controls. In cohort II, serum exosomal miR-200c expression was significantly lower in the BC group than in the control and benign breast disease (BBD) groups, whereas miR-200c expression in the BBD group was not statistically different from that in the control group. ROC analyses in both independent cohorts confirmed that serum exosomal miR-200c could differentiate between patients with and without BC disease and could be used as an early diagnostic marker for BC disease. Conclusion Serum exosome miR-200c can be used as a potential biomarker for the diagnosis of BC, and combined with conventional serum diagnostic markers AFP, CA125 and CA153 can help to improve diagnostic efficiency.

Prospects for breast cancer immunotherapy using microRNAs and transposable elements as objects.

One of the directions in treatment of chemoresistant breast cancer (BC) may include new methods of activating the immune response against tumor cells. Clinically used checkpoint inhibition using antibodies to PD-1 and PD-L1 works in some patients, but the lack of biomarkers means number of respondents is low. The possibility of combining this method with chemotherapy is limited by an increased risk of toxic liver damage, development of immune-related pneumonitis, and thyroid dysfunction. This article includes introduction into the clinic of new methods of immunotherapy for BC, among which epigenetic activation of retroelements, double-stranded transcripts of which stimulate the interferon response against the tumor, is promising. For this purpose, inhibitors of DNA methyltransferase*, histone deacetylase* and histone methyltransferase* are used (* subtitles in the main text). Their antitumor effect is also mediated by removal of repressive epigenetic marks from tumor suppressor genes. However, numerous studies have proven the role of retroelements in the carcinogenesis of various malignant neoplasms, including BC. Moreover, endogenous retroviruses HERV-K and LINE1 retrotransposons are planned to be used as diagnostic biomarkers for BC. Therefore, a rational approach to using viral mimicry in antitumor therapy of BC may be the simultaneous suppression of specific retrotransposons (drivers for carcinogenesis) using reverse transcriptase inhibitors and silencing of specific transposons involved in carcinogenesis using complementary microRNAs. To determine possible pathways of influence in this direction, 35 specific transposon-derived microRNAs* changes in BC were identified, which can become guides for targeted therapy of BC.

ECM1 and ANXA1 in urinary extracellular vesicles serve as biomarkers for breast cancer.

Although urinary extracellular vesicles (uEVs) have been extensively studied in various cancers, their involvement in breast cancer (BC) remains largely unexplored. The non-invasive nature of urine as a biofluid and its abundant protein content offer considerable potential for the early detection of breast cancer. This study analyzed the proteomic profiles of uEVs from BC patients and healthy controls (HC). The dysregulation of ECM1 and ANXA1 in the uEVs was validated in a larger cohort of 128 BC patients, 25 HC and 25 benign breast nodules (BBN) by chemiluminescence assay (CLIA). The expression levels of ECM1 and ANXA1 were also confirmed in the uEVs of MMTV-PyMT transgenic breast cancer mouse models. LC-MS/MS analysis identified 571 dysregulated proteins in the uEVs of BC patients. ECM1 and ANXA1 were selected for validation in 128 BC patients, 25 HC and 25 BBN using CLIA, as their fold change showed a significant difference of more than 10 with p-value<0.05. Protein levels of ECM1 and ANXA1 in uEVs were significantly increased in BC patients. In addition, the protein levels of ECM1 and ANXA1 in the uEVs of MMTV-PyMT transgenic mice were observed to increase progressively with the progression of breast cancer. We developed a simple and purification-free assay platform to isolate uEVs and quantitatively detect ECM1 and ANXA1 in uEVs by WGA-coupled magnetic beads and CLIA. Our results suggest that ECM1 and ANXA1 in uEVs could potentially serve as diagnostic biomarkers for breast cancer.

Down regulation of C1q tumor necrosis factor-related protein 6 is associated with increased risk of breast cancer

C1q tumor necrosis factor-related protein 6 (CTRP6), a member of the C1q tumor necrosis factor-related protein (CTRP) family, is reported to be associated with the progression of different malignancies, however, its expression levels and role in breast cancer (BC) are yet unknown. In this study, we investigated the levels of circulating CTRP6 in BC patients and evaluated its role as a potential diagnostic biomarker in BC patients. Then we investigated the effect of recombinant CTRP6 on cellular viability in MCF-7 cells along with its effects on the expression of inflammatory cytokines, interleukin 6 (IL-6), tumor necrosis factor alpha (TNF-α) in addition to the expression of vascular endothelial growth factor (VEGF) as a marker of angiogenesis. Our results showed decreased expression of circulating CTRP6 in BC patients with an inverse correlation between CTRP6 and IL-6, TNF-α and VEGF levels. Besides, Receiver operating characteristic (ROC) curve showed that the assessment of CTRP6 levels could be used to predict BC. Moreover, treatment of MCF-7 cells with recombinant CTRP6 protein reduced cellular viability and decreased IL-6, TNF-α and VEGF expression. In conclusion, these results provide new insights into the role of CTRP6 in BC pathogenesis and suggest its potential use as a novel diagnostic biomarker of BC.

Correlation of serum NFкB levels with neutrophil-lymphocyte ratio and platelet -lymphocyte ratio in breast cancer patients

ObjectiveThe main objective of this study was to analyze the serum levels of Nuclear factor-kappa B (NFкB) in breast cancer as compared to age-matched healthy individuals. It also aimed to investigate variations in NFкB levels across stages, types of breast cancer and also its correlation with Neutrophil-Lymphocyte Ratio (NLR) and Platelet-Lymphocyte Ratio (PLR). MethodologyBlood samples of 40 female breast cancer patients and 33 healthy controls were collected in anticoagulant and plain tubes. Hematological parameters were evaluated with an automatic analyzer, and NFкB levels were measured using ELISA. Statistical analysis was performed with GraphPad Prism 8 software. ResultsSignificant elevation of serum NFкB levels (p < 0.0001) was observed in breast cancer patients when compared to the healthy females. Subtype analysis indicated higher NFкB levels in Triple Negative Breast Cancer (TNBC), suggesting a potential role in the aggressiveness of this subtype. Correlation analysis with hematological parameters, including NLR and PLR, showed weak associations. However, Receiver Operating Characteristic (ROC) analysis indicated the promising role of NFкB as a diagnostic biomarker for breast cancer with a sensitivity of 75 % and specificity of 74.8 % at a cutoff value of 0.447 ng/ml. ConclusionSerum NFκB levels were significantly elevated in breast cancer patients when compared to healthy individuals, suggesting its potential as a diagnostic biomarker for the disease. While weak correlations were observed with hematological parameters like NLR, and PLR in breast cancer patients, the study highlights the promising diagnostic potential of NFκB and its significant association with breast cancer.

Spatial and single-cell explorations uncover prognostic significance and immunological functions of mitochondrial calcium uniporter in breast cancer

The mitochondrial calcium uniporter (MCU) is a transmembrane protein facilitating the entry of calcium ions into mitochondria from the cell cytosol. Maintaining calcium balance is crucial for enhancing cellular energy supply and regulating cell death. The interplay of calcium balance through MCU and the sodium-calcium exchanger is known, but its regulation in the breast cancer tumor microenvironment remains elusive. Further investigations are warranted to explore MCU’s potential in BRCA clinical pathology, tumor immune microenvironment, and precision oncology. Our study, employing a multi-omics approach, identifies MCU as an independent diagnostic biomarker for breast cancer (BRCA), correlated with advanced clinical status and poor overall survival. Utilizing public datasets from GEO and TCGA, we discern differentially expressed genes in BRCA and examine their associations with immune gene expression, overall survival, tumor stage, gene mutation status, and infiltrating immune cells. Spatial transcriptomics is employed to investigate MCU gene expression in various regions of BRCA, while spatial transcriptomics and single-cell RNA-sequencing methods explore the correlation between MCUs and immune cells. Our findings are validated through the analysis of 59 BRCA patient samples, utilizing immunohistochemistry and bioinformatics to examine the relationship between MCU expression, clinicopathological features, and prognosis. The study uncovers the expression of key gene regulators in BRCA associated with genetic variations, deletions, and the tumor microenvironment. Mutations in these regulators positively correlate with different immune cells in six immune datasets, playing a pivotal role in immune cell infiltration in BRCA. Notably, high MCU performance is linked to CD8 + T cells infiltration in BRCA. Furthermore, pharmacogenomic analysis of BRCA cell lines indicates that MCU inactivation is associated with increased sensitivity to specific small molecule drugs. Our findings suggest that MCU alterations may be linked to BRCA progression, unveiling new diagnostic and prognostic implications for MCU in BRCA. The study underscores MCU's role in the tumor immune microenvironment and cell cycle progression, positioning it as a potential tool for BRCA precision medicine and drug screening.

UTRN as a potential biomarker in breast cancer: a comprehensive bioinformatics and in vitro study

Utrophin (UTRN), known as a tumor suppressor, potentially regulates tumor development and the immune microenvironment. However, its impact on breast cancer’s development and treatment remains unstudied. We conducted a thorough examination of UTRN using both bioinformatic and in vitro experiments in this study. We discovered UTRN expression decreased in breast cancer compared to standard samples. High UTRN expression correlated with better prognosis. Drug sensitivity tests and RT-qPCR assays revealed UTRN’s pivotal role in tamoxifen resistance. Furthermore, the Kruskal–Wallis rank test indicated UTRN’s potential as a valuable diagnostic biomarker for breast cancer and its utility in detecting T stage of breast cancer. Additionally, our results demonstrated UTRN’s close association with immune cells, inhibitors, stimulators, receptors, and chemokines in breast cancer (BRCA). This research provides a novel perspective on UTRN’s role in breast cancer’s prognostic and therapeutic value. Low UTRN expression may contribute to tamoxifen resistance and a poor prognosis. Specifically, UTRN can improve clinical decision-making and raise the diagnosis accuracy of breast cancer.

Plasma Thioredoxin Reductase as a Potential Diagnostic Biomarker for Breast Cancer

BackgroundEarly diagnosis of breast cancer is critical to the treatment and prognosis of breast cancer patients. Our aim is to explore more practical and effective diagnostic methods to facilitate early treatment and improve prognosis for breast cancer patients. Materials and MethodsThe Mann–Whitney U test, receiver operating characteristic curve, Youden index, Chi-square test, and Fisher's exact test were used to determine whether plasma thioredoxin reductase (TrxR) could be used for the clinical diagnosis of breast cancer. The Wilcoxon signed-rank test was used to validate the prognostic potential of plasma TrxR activity assessment. ResultsA total of 761 patients were included, including 537 cases of breast cancer and 224 cases of benign breast diseases. Plasma TrxR activity in the breast cancer group [8.0 (6.0, 9.45) U/mL] was significantly higher than that in the benign group [3.05 (1.20, 6.275) U/mL]. The diagnostic efficiency of TrxR for breast cancer was higher than that of other conventional breast cancer biomarkers, with an area under the curve of 0.821 (95% CI = 0.791-0.852). In addition, TrxR can be used in combination with conventional tumor markers to further improve the diagnostic efficiency. The optimal TrxR threshold for identifying benign and malignant diseases is 7.45 U/mL. We detected plasma TrxR activity and serum tumor markers before and after antitumor therapies in 333 breast cancer patients and found that their trends were basically the same, with a significant decrease in plasma TrxR activity after treatment. ConclusionPlasma TrxR activity can be used as a suitable biomarker for breast cancer diagnosis and efficacy assessment.

Serum miR-16 and CA15.3 combination as early diagnostic biomarkers for breast cancer in Egyptian females

Serum miR-16 and CA15.3 combination as early diagnostic biomarkers for breast cancer in Egyptian females

Integrative Bioinformatics Analysis Reveals Potential Target Genes and PTEN Signaling in Breast Cancer and Effect of Zingiber officinale (Ginger) and Allium sativum (Garlic) extract on It.

Breast cancer is the most common type of cancer in women. The construction of a competing gene network is an important step in the identification of the role of hub genes in breast cancers. In the current research, we used a number of bioinformatics tools to construct this network in breast cancer and investigated the combined effect of garlic and ginger on mice model of breast cancer. We chose female mice weighing 18-20 g that were divided into 7 groups including; the cancer group receiving normal saline, different doses of ginger extract (100 and 500 mg/kg), different doses of garlic (50 and 100 mg/kg), tamoxifen (10 mg/ kg) and simultaneous garlic (100 mg/kg) and ginger (500 mg/kg) for 3 weeks intraperitoneal. Then we anesthetized the mice, isolated the tumor, and determined its size. Glutathione reductase and peroxidase levels and HER2, PTEN, and Cullin3 genes expression were measured. We identified 20 hub genes for breast cancer. In animal phase we found that tumor size in all mice receiving garlic and ginger showed a significant decrease compared to the control. Glutathione reductase showed a significant increase in all groups, especially in ginger 500 and combined groups. Glutathione peroxidase increased almost in all groups, especially in ginger 500. Expression of HER2 decreased in all treated groups. Expression of PTEN increased just in the combined group. Taken together, we introduce a number of novel promising diagnostic biomarkers for breast cancer. The use of garlic and ginger in the treatment of cancer can be useful. This action is probably through the antioxidant mechanism, and regulation of the expression of cancer related genes such as PTEN.

Exosomal microRNA-92b Is a Diagnostic Biomarker in Breast Cancer and Targets Survival-Related MTSS1L to Promote Tumorigenesis.

Exosomal microRNAs (miRNAs) are novel, non-invasive biomarkers for facilitating communication and diagnosing cancer. However, only a few studies have investigated their function and role in the clinical diagnosis of breast cancer. To address this gap, we established a stable cell line, MDA-MB-231-CD63-RFP, and recruited 112 female participants for serum collection. We screened 88 exosomal miRNAs identified through microarray analysis of 231-CD63 and literature screening using real-time PCR; only exosomal miR-92b-5p was significantly increased in patients with breast cancer. It had a significant correlation with stage and discriminated patients from the control with an AUC of 0.787. Exosomal miR-92b-5p impacted the migration, adhesion, and spreading ability of normal human mammary epithelial recipient cells through the downregulation of the actin dynamics regulator MTSS1L. In clinical breast cancer tissue, the expression of MTSS1L was significantly inversely correlated with tissue miR-92b-5p, and high expression of MTSS1L was associated with better 10-year overall survival rates in patients undergoing hormone therapy. In summary, our studies demonstrated that exosomal miR-92b-5p might function as a non-invasive body fluid biomarker for breast cancer detection and provide a novel therapeutic strategy in the axis of miR-92b-5p to MTSS1L for controlling metastasis and improving patient survival.

Comparative profiling by data-independent acquisition mass spectrometry reveals featured plasma proteins in breast cancer: a pilot study.

Breast cancer is known to be influenced by genetic and environmental factors, and several susceptibility genes have been discovered. Still, the majority of genetic contributors remain unknown. We aimed to analyze the plasma proteome of breast cancer patients in comparison to healthy individuals to identify differences in protein expression profiles and discover novel biomarkers. This pilot study was conducted using bioresources from Seoul National University Bundang Hospital's Human Bioresource Center. Serum samples from 10 breast cancer patients and 10 healthy controls were obtained. Liquid chromatography-mass spectrometry analysis was performed to identify differentially expressed proteins. We identified 891 proteins; 805 were expressed in the breast cancer group and 882 in the control group. Gene set enrichment and differential expression analysis identified 30 upregulated and 100 downregulated proteins in breast cancer. Among these, 10 proteins were selected as potential biomarkers. Three proteins were upregulated in breast cancer patients, including cluster of differentiation 44, eukaryotic translation initiation factor 2-α kinase 3, and fibronectin 1. Seven proteins downregulated in breast cancer patients were also selected: glyceraldehyde-3-phosphate dehydrogenase, α-enolase, heat shock protein member 8, integrin-linked kinase, tissue inhibitor of metalloproteinases-1, vasodilator-stimulated phosphoprotein, and 14-3-3 protein gamma. All proteins had been previously reported to be related to tumor development and progression. The findings suggest that plasma proteome profiling can reveal potential diagnostic biomarkers for breast cancer and may contribute to early detection and personalized treatment strategies. A further validation study with a larger sample cohort of breast cancer patients is planned.

Comprehensive evaluation of cell death-related genes as novel diagnostic biomarkers for breast cancer

BackgroundBreast cancer (BRCA) ranks first among cancers in terms of incidence and mortality rates in women, primarily owing to metastasis, chemo-resistance, and heterogeneity. To predict long-term prognosis and design novel therapies for BRCA, more sensitive markers need to be explored. MethodsData from 1089 BRCA patients were downloaded from TCGA database. Pearson's correlation analysis and univariate and multivariate Cox regression analyses were performed to assess the role of cell death-related genes (CDGs) in predicting BRCA prognosis. Kaplan–Meier survival curves were generated to compare the overall survival in the two subgroups. A nomogram was constructed using risk scores based on the five CDGs and other clinicopathological features. CCK-8, EdU incorporation, and colony formation assays were performed to verify the inhibitory effect of NFKBIA on BRCA cell proliferation. Transwell assay, flow cytometry, and immunohistochemistry analyses were performed to ascertain the biological function of NFKBIA. ResultsFive differentially expressed CDGs were detected among 156 CDGs. The risk score for each patient was then calculated based on the expression levels of the five CDGs. Distinct differences in immune infiltration, expression of immune-oncological targets, mutation status, and half-maximal inhibitory concentration values of some targeted drugs were observed between the high- and low-risk groups. Finally, in vitro cell experiments verified that NFKBIA overexpression suppresses the proliferation and migration of BRCA cells. ConclusionsOur study revealed that some CDGs, especially NFKBIA, could serve as sensitive markers for predicting the prognosis of patients with BRCA and designing more personalized clinical therapies.

Identification of early diagnostic biomarkers for breast cancer through bioinformatics analysis.

In the realm of clinical practice, there is currently an insufficiency of distinct biomarkers available for the detection of breast cancer. It is of utmost importance to promptly employ bioinformatics methodologies to investigate prospective biomarkers for breast cancer, with the ultimate goal of achieving early diagnosis of the disease. The initial phase of this investigation involved the identification of 2 breast cancer gene chips meeting the specified criteria within the gene expression omnibus database. Subsequently, paired data analysis was conducted on these datasets, leading to the identification of differentially expressed genes (DEGs). In addition, this study executed Gene Ontology enrichment analysis and Kyoto encyclopedia of genes and genomes pathway enrichment analysis. The subsequent stage involved the construction of a protein-protein interaction network graph using the STRING website and Cytoscape software, facilitating the calculation of Hub genes. Lastly, the UALCAN database and Kaplan-Meier survival plots were utilized to perform differential expression and survival analysis on the selected Hub genes. A total of 733 DEGs were identified from the combined analysis of 2 datasets. Among these DEGs, 441 genes were found to be downregulated, while 292 genes were upregulated. The selected DEGs underwent comprehensive analysis, including gene ontology enrichment analysis, Kyoto encyclopedia of genes and genomes pathway enrichment analysis, and establishing a protein-protein interaction network. As a result, 10 Hub genes closely associated with early diagnosis of breast cancer were identified: PDZ-binding kinase, cell cycle protein A2, cell division cycle-associated protein 8, maternal embryonic leucine zipper kinase, nucleolar and spindle-associated protein 1, BIRC5, cell cycle protein B2, hyaluronan-mediated motility receptor, mitotic arrest deficient 2-like 1, and protein regulator of cytokinesis 1. The findings of this study unveiled the significant involvement of the identified 10 Hub genes in facilitating the growth and proliferation of cancer cells, particularly cell cycle protein A2, cell division cycle-associated protein 8, maternal embryonic leucine zipper kinase, nucleolar and spindle-associated protein 1, hyaluronan-mediated motility receptor, and protein regulator of cytokinesis 1, which demonstrated a more pronounced connection with the onset and progression of breast cancer. Further analysis through differential expression and survival analysis reaffirmed their strong correlation with the incidence of breast cancer. Consequently, the investigation of these 10 pertinent Hub genes presents novel prospects for potential biomarkers and valuable insights into the early diagnosis of breast cancer.

GLS as a diagnostic biomarker in breast cancer: in-silico, in-situ, and in-vitro insights.

Recently, a novel programmed cell death mechanism, Cuproptosis, has been discovered and found to play an important role in the development and progression of diverse tumors. In the present study, we comprehensively investigated the core gene of this mechanism, GLS, in breast cancer. Bulk RNA sequencing data were curated from the TCGA repository to investigate the aberrant expression of GLS over diverse cancer types. Then, we examined its efficacy as a diagnostic biomarker in breast cancer by Area Under Curve (AUC) of the Receiver Operative Characteristic (ROC) curve. Furthermore, by applying siRNA technique, we knocked down the GLS expression level in cancerous cell lines, measuring the corresponding effects on cell proliferation and metastasis. Afterward, we explored the potential implications of GLS expression in the tumor immune microenvironment quantitatively by using several R packages and algorithms, including ESTIMATE, CIBERSORT, etc. Pan-cancer analysis suggested that GLS was aberrantly over-expressed in many cancer types, with breast cancer being typical. More in-depth analyses revealed the expression of GLS exerted a high ROC-AUC value in breast cancer diagnosis. Through the knock-down of GLS expression, it was found that GLS expression was strongly relevant to the growth and metastasis of tumor. Furthermore, it was also found to be correlated with the immune tumor microenvironment. We highlighted that GLS expression might be applicable as a diagnostic biomarker in breast cancer and possess significant implications in the growth and metastasis of tumor and the immune tumor microenvironment, sharing new insights into ontological and personalized medicine.

Identification of four candidates circulating microRNAs in plasma as a potential biomarker for early-stage breast cancer diagnosis in Vietnamese women

Breast cancer is the most commonly occurring malignant neoplasm among the female population. This study aims to ascertain novel biomarkers that may prove advantageous in the early detection of breast cancer. The present investigation involved a comparative analysis of the plasma expression of four distinct microRNA (namely, miR-425-5p, miR-142-3p, miR-9-3p and miR-15b-5p) in a cohort of 80 Vietnamese patients who were newly diagnosed with breast cancer. The expression levels of these microRNA were compared with those of 80 healthy individuals who served as controls. The plasma total RNA was extracted and the miRNA expression levels were assessed using Stem-loop RT-qPCR followed by statistical analysis. According to the findings of our study, the plasma levels of four microRNAs namely miR-425-5p, miR-142-3p, miR-9-3p and miR-15b-5p, were significantly reduced in both breast cancer patients in stage 0-I and the general breast cancer patient population as compared to healthy controls. The diagnostic accuracy of both miR-9-3p levels and miR-15b-5p levels was satisfactory with 74% and 88% values respectively. The combined effect of miR-425-5p/miR-142-3p/miR-9-3p/miR-15b-5p revealed the highest level of diagnostic precision, attaining a rate of 98% and an area under the curve value of 0.98 (with a sensitivity of 87.5% and specificity of 100%). In summary, the microRNAs miR-425-5p, miR-142-3p, miR-9-3p and miR-15b-5p exhibit potential as non-invasive diagnostic biomarkers for breast cancer, particularly in the initial stages of the disease.

Peripheral blood mononuclear cell derived biomarker detection using eXplainable Artificial Intelligence (XAI) provides better diagnosis of breast cancer

The incidence and mortality rate of breast cancer increases yearly by an average of 1.44 % and 0.23 %, respectively. Till 2021, there were 7.8 million women who had been diagnosed with breast cancer within 5 years. Biopsies of tumors are often expensive and invasive and raise the risk of serious complications like infection, excessive bleeding, and puncture damage to nearby tissues and organs. Early detection biomarkers are often variably expressed in different patients and may even be below the detection level at an early stage. Hence PBMC that shows alteration in gene profile as a result of interaction with tumor antigens may serve as a better early detection biomarker. Also, such alterations in immune gene profile in PBMCs are more prone to detection despite variability in different breast cancer mutants.This study aimed to identify potential diagnostic biomarkers for breast cancer using eXplainable Artificial Intelligence (XAI) on XGBoost machine learning (ML) models trained on a binary classification dataset containing the expression data of PBMCs from 252 breast cancer patients and 194 healthy women.After effectively adding SHAP values further into the XGBoost model, ten important genes related to breast cancer development were discovered to be effective potential biomarkers. Our studies showed that SVIP, BEND3, MDGA2, LEF1-AS1, PRM1, TEX14, MZB1, TMIGD2, KIT, and FKBP7 are key genes that impact model prediction. These genes may serve as early, non-invasive diagnostic and prognostic biomarkers for breast cancer patients.